Evaluation of oyster exposure experiments

knitr::opts_chunk$set(echo = TRUE, warning = F, message = F, fig.path = 'figs/', dev.args = list(family = 'serif'))

library(tidyverse)
library(patchwork)
library(ggbeeswarm)
library(psycho)
library(lmerTest)
library(hrbrthemes)
library(kableExtra)
library(shiny)

source('R/funcs.R')

data(allexp)
data(bymods)
data(wtmods)

Number of folds

Raw data

yvar <- 'Number of folds'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of folds vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.74	0.18	4	32.45	11.48	0.00
week	0.01	0.01	2	30.48	0.38	0.69

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of folds vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.63	0.16	4	25.69	9.92	0.00
week	0.01	0.01	2	24.16	0.42	0.66
trt:week	0.07	0.01	8	25.46	0.58	0.79

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of folds vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.66	0.17	4	38.14	8.31	0.00
week	0.01	0.00	2	36.80	0.21	0.81

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of folds vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.73	0.18	4	31.25	9.19	0.00
week	0.01	0.01	2	30.19	0.36	0.70
trt:week	0.23	0.03	8	31.05	1.42	0.23

dat %>% 
  pull(plomod)

Number of irregularites

Raw data

yvar <- 'Number of irregularities'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of irregularities vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.31	0.08	4	37.07	1.68	0.18
week	0.06	0.03	2	31.63	0.64	0.54

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of irregularities vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.38	0.10	4	26.01	2.24	0.09
week	0.07	0.03	2	23.62	0.80	0.46
trt:week	0.53	0.07	8	26.22	1.54	0.19

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of irregularities vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.45	0.11	4	38.34	4.00	0.01
week	0.02	0.01	2	36.72	0.32	0.73

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Number of irregularities vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.70	0.18	4	27.51	6.08	0.00
week	0.03	0.02	2	26.70	0.53	0.60
trt:week	0.78	0.10	8	27.19	3.40	0.01

dat %>% 
  pull(plomod)

Total observations (dissolution)

Raw data

yvar <- 'Total observations'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Total observations vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	1.16	0.29	4	39.12	1.19	0.33
week	0.14	0.07	2	35.48	0.30	0.75

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Total observations vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	1.42	0.36	4	31.93	1.48	0.23
week	0.16	0.08	2	29.77	0.33	0.72
trt:week	2.37	0.30	8	31.83	1.23	0.31

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Total observations vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	1.55	0.39	4	36.54	1.16	0.34
week	2.40	1.20	2	34.90	3.61	0.04

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Total observations vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	1.87	0.47	4	28.70	1.40	0.26
week	2.71	1.36	2	27.63	4.07	0.03
trt:week	4.51	0.56	8	28.56	1.69	0.14

dat %>% 
  pull(plomod)

Dissolution score

Raw data

yvar <- 'Dissolution score (0-3)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Dissolution score (0-3) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	3.90	0.97	4	39.04	9.20	0.00
week	0.07	0.03	2	36.14	0.32	0.73

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Dissolution score (0-3) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	4.78	1.19	4	28.14	10.96	0.00
week	0.05	0.02	2	26.69	0.22	0.81
trt:week	1.37	0.17	8	27.81	1.58	0.18

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Dissolution score (0-3) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	3.24	0.81	4	37.38	10.71	0.0
week	0.14	0.07	2	36.11	0.95	0.4

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Dissolution score (0-3) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	3.30	0.82	4	27.73	10.76	0.00
week	0.15	0.07	2	26.72	0.97	0.39
trt:week	0.49	0.06	8	27.56	0.80	0.61

dat %>% 
  pull(plomod)

Shell weight

Raw data

yvar <- 'Shell weight (g)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Shell weight (g) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.05	0.01	4	59.65	0.33	0.86
week	0.10	0.05	2	60.13	1.31	0.28

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Shell weight (g) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.05	0.01	4	50.58	0.34	0.85
week	0.09	0.05	2	51.98	1.23	0.30
trt:week	0.27	0.03	8	52.01	0.90	0.52

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Shell weight (g) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.05	0.01	4	53.91	1.29	0.29
week	0.03	0.01	2	53.07	1.28	0.29

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Shell weight (g) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.06	0.01	4	43.46	1.44	0.24
week	0.03	0.01	2	43.60	1.34	0.27
trt:week	0.11	0.01	8	43.61	1.39	0.23

dat %>% 
  pull(plomod)

Tissue weight

Raw data

yvar <- 'Tissue weight (g)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Tissue weight (g) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0	0	4	59.92	0.59	0.67
week	0	0	2	60.38	1.29	0.28

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Tissue weight (g) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.00	0	4	51.28	0.62	0.65
week	0.00	0	2	52.70	1.23	0.30
trt:week	0.01	0	8	52.73	0.68	0.71

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Tissue weight (g) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0	0	4	51.40	0.71	0.59
week	0	0	2	50.57	0.86	0.43

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Tissue weight (g) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.00	0	4	41.32	0.87	0.49
week	0.00	0	2	41.46	0.92	0.41
trt:week	0.01	0	8	41.48	1.32	0.26

dat %>% 
  pull(plomod)

Whole weight

Raw data

yvar <- 'Whole weight (g)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Whole weight (g) vs week + treatment

	Df	Deviance	Resid. Df	Resid. Dev
NULL	NA	NA	286	21.97
trt	4	0.64	282	21.33
week	2	0.92	280	20.41

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Whole weight (g) vs week x treatment

	Df	Deviance	Resid. Df	Resid. Dev
NULL	NA	NA	286	21.97
trt	4	0.64	282	21.33
week	2	0.92	280	20.41
trt:week	8	1.03	272	19.38

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Whole weight (g) vs week + treatment

	Df	Deviance	Resid. Df	Resid. Dev
NULL	NA	NA	275	7.04
trt	4	0.15	271	6.90
week	2	0.15	269	6.75

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Whole weight (g) vs week x treatment

	Df	Deviance	Resid. Df	Resid. Dev
NULL	NA	NA	275	7.04
trt	4	0.15	271	6.90
week	2	0.15	269	6.75
trt:week	8	1.20	261	5.54

dat %>% 
  pull(plomod)

Delta length

Raw data

yvar <- 'Delta length (cm)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta length (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.03	0.01	4	37.30	0.29	0.88
week	0.14	0.14	1	37.49	5.91	0.02

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta length (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.02	0.01	4	34.13	0.23	0.92
week	0.11	0.11	1	34.10	4.62	0.04
trt:week	0.08	0.02	4	34.13	0.83	0.52

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta length (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.05	0.01	4	37.78	0.59	0.67
week	0.01	0.01	1	37.78	0.25	0.62

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta length (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.19	0.05	4	36.15	2.14	0.10
week	0.08	0.08	1	38.49	3.53	0.07
trt:week	0.29	0.07	4	36.15	3.36	0.02

dat %>% 
  pull(plomod)

Delta width

Raw data

yvar <- 'Delta width (cm)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta width (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.02	0.01	4	40.04	0.25	0.91
week	0.02	0.02	1	40.20	1.03	0.32

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta width (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.02	0.01	4	35.76	0.26	0.90
week	0.02	0.02	1	35.72	0.73	0.40
trt:week	0.07	0.02	4	35.76	0.73	0.58

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta width (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.04	0.01	4	34.37	0.51	0.73
week	0.00	0.00	1	34.68	0.05	0.83

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Delta width (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.07	0.02	4	32.88	0.92	0.47
week	0.01	0.01	1	36.05	0.29	0.59
trt:week	0.14	0.03	4	32.88	1.75	0.16

dat %>% 
  pull(plomod)

Final length

Raw data

yvar <- 'Final length (cm)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final length (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.25	0.06	4	46.59	0.74	0.57
week	0.13	0.06	2	46.21	0.75	0.48

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final length (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.29	0.07	4	38.11	0.89	0.48
week	0.09	0.04	2	38.24	0.53	0.59
trt:week	0.64	0.08	8	38.26	0.96	0.48

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final length (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.17	0.04	4	47.20	0.46	0.76
week	0.13	0.07	2	45.87	0.71	0.50

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final length (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.23	0.06	4	38.72	0.63	0.65
week	0.22	0.11	2	39.77	1.18	0.32
trt:week	0.75	0.09	8	38.71	1.01	0.45

dat %>% 
  pull(plomod)

Final width

Raw data

yvar <- 'Final width (cm)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final width (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.19	0.05	4	46.52	0.77	0.55
week	0.09	0.04	2	46.12	0.71	0.50

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final width (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.18	0.04	4	37.96	0.74	0.57
week	0.07	0.04	2	38.10	0.59	0.56
trt:week	0.39	0.05	8	38.12	0.81	0.59

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final width (cm) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.07	0.02	4	47.55	0.36	0.84
week	0.19	0.09	2	46.03	1.79	0.18

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Final width (cm) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	0.16	0.04	4	38.74	0.79	0.54
week	0.23	0.11	2	40.01	2.18	0.13
trt:week	0.52	0.06	8	38.65	1.25	0.30

dat %>% 
  pull(plomod)

Respiration

Raw data

yvar <- 'Respiration (umol/hr/g)'

toplo <- allexp %>% 
  filter(var %in% yvar)

p <- ggplot(toplo, aes(x = factor(week), y = val, colour = species, fill = species)) + 
  geom_boxplot(outlier.shape = NA, alpha = 0.1) + 
  geom_point(aes(group = species), position = position_jitterdodge(jitter.width = 0.1), size = 2, alpha = 0.6) + 
  theme_ipsum_rc() + 
  facet_grid(trt~ .) + 
  scale_colour_ipsum() + 
  scale_fill_ipsum() + 
  theme(legend.title = element_blank()) + 
  labs(x = 'Exposure week', y = yvar)

p

Models by week

Olympia oyster

bymods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Pacific oyster

bymods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar) %>% 
  pull(plomod)

Models with week

Olympia oyster

dat <- wtmods %>% 
  filter(species == 'Olympia') %>% 
  filter(var == yvar)

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Respiration (umol/hr/g) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	16.68	4.17	4	51.04	0.34	0.85
week	9.67	4.83	2	55.99	0.40	0.67

dat %>% 
  filter(species == 'Olympia') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Respiration (umol/hr/g) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	13.93	3.48	4	44.51	0.29	0.88
week	10.23	5.12	2	46.96	0.42	0.66
trt:week	64.95	8.12	8	47.14	0.67	0.72

dat %>% 
  pull(plomod)

Pacific oyster

dat <- wtmods %>% 
  filter(species == 'Pacific') %>% 
  filter(var == yvar)
         
dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomodnoint) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week + treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Respiration (umol/hr/g) vs week + treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	40.25	10.06	4	53.53	0.73	0.58
week	11.31	5.66	2	52.35	0.41	0.67

dat %>% 
  filter(species == 'Pacific') %>% 
  pull(anomod) %>% 
  .[[1]] %>% 
  knitr::kable(format = 'html', digits = 2, caption = paste0(yvar, ' vs week x treatment')) %>%
  kable_styling(full_width = T, font_size = 14) %>% 
  HTML

Respiration (umol/hr/g) vs week x treatment

	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
trt	37.54	9.39	4	45.50	0.69	0.61
week	9.84	4.92	2	44.45	0.36	0.70
trt:week	54.96	6.87	8	45.48	0.50	0.85

dat %>% 
  pull(plomod)